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OPENSEQ.org
2g38
Genes: A B A+B
Length: 99 198 289
Sequences: 407 580 202
Seq/Len: 4.11 2.93 0.7
MirrorTree (Pazo et al. 2001) 0.36
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.07 0.16 0.35
2 0.10 0.19 0.38
5 0.13 0.20 0.46
10 0.15 0.23 0.59
20 0.18 0.26 0.68
100 0.25 0.32 0.97
∞ 0.27 0.37 0.99
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on HHsearch results which uses the overall probability and per-site alignment confidence. Inter-chain contacts in the pdb are in shades of red. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
38_A 109_I 1.69 0.79 0.03
42_P 158_S 1.54 0.69 0.02
6_T 61_V 1.53 0.69 0.02
90_A 108_Q 1.29 0.49 0.01
25_A 21_P 1.26 0.47 0.01
42_P 23_S 1.17 0.40 0.01
13_V 62_M 1.17 0.40 0.01
76_F 61_V 1.15 0.38 0.01
59_A 37_E 1.15 0.38 0.01
58_Y 19_P 1.14 0.37 0.01
22_R 71_F 1.12 0.36 0.01
46_L 14_N 1.11 0.35 0.01
59_A 190_S 1.11 0.34 0.01
72_V 125_L 1.09 0.34 0.01
66_I 90_H 1.09 0.33 0.01
68_A 61_V 1.08 0.32 0.01
74_E 179_L 1.06 0.31 0.01
6_T 47_R 1.05 0.31 0.01
71_V 94_R 1.05 0.30 0.01
59_A 167_W 1.05 0.30 0.01
82_T 50_L 1.04 0.30 0.01
36_T 60_V 1.04 0.29 0.01
62_Y 65_M 1.01 0.28 0.00
62_Y 78_L 1.00 0.27 0.00
86_K 10_V 0.99 0.26 0.00
35_M 35_D 0.98 0.26 0.00
88_A 31_W 0.98 0.26 0.00
59_A 155_L 0.97 0.25 0.00
58_Y 62_M 0.97 0.25 0.00
46_L 180_V 0.96 0.24 0.00
16_T 93_V 0.95 0.24 0.00
14_A 48_T 0.95 0.24 0.00
51_A 92_I 0.95 0.24 0.00
29_D 14_N 0.95 0.24 0.00
2_S 192_T 0.95 0.24 0.00
69_A 27_A 0.95 0.24 0.00
70_A 62_M 0.94 0.23 0.00
26_I 83_S 0.93 0.23 0.00
61_K 85_V 0.92 0.22 0.00
16_T 61_V 0.92 0.22 0.00
60_R 35_D 0.92 0.22 0.00
82_T 10_V 0.91 0.21 0.00
32_V 128_F 0.90 0.21 0.00
2_S 185_P 0.90 0.20 0.00
19_R 24_M 0.89 0.20 0.00
74_E 60_V 0.89 0.20 0.00
11_L 13_A 0.89 0.20 0.00
60_R 51_S 0.89 0.20 0.00
71_V 66_E 0.88 0.20 0.00
17_E 29_R 0.88 0.20 0.00
96_K 85_V 0.88 0.19 0.00
56_V 96_Y 0.87 0.19 0.00
17_E 172_P 0.87 0.19 0.00
59_A 114_A 0.85 0.18 0.00
25_A 41_V 0.85 0.18 0.00
60_R 21_P 0.85 0.18 0.00
43_A 92_I 0.85 0.18 0.00
24_R 65_M 0.85 0.18 0.00
58_Y 96_Y 0.84 0.18 0.00
57_E 159_D 0.84 0.18 0.00
92_A 19_P 0.84 0.18 0.00
5_I 40_A 0.84 0.18 0.00
54_F 19_P 0.83 0.17 0.00
39_V 36_V 0.83 0.17 0.00
26_I 155_L 0.83 0.17 0.00
81_T 60_V 0.82 0.17 0.00
33_A 162_S 0.82 0.17 0.00
32_V 155_L 0.82 0.17 0.00
27_Q 24_M 0.82 0.17 0.00
91_E 97_E 0.82 0.17 0.00
10_A 171_P 0.82 0.17 0.00
81_T 17_A 0.82 0.17 0.00
28_S 37_E 0.82 0.17 0.00
76_F 41_V 0.82 0.17 0.00
72_V 171_P 0.82 0.17 0.00
71_V 183_V 0.81 0.17 0.00
78_H 152_D 0.81 0.16 0.00
62_Y 34_L 0.81 0.16 0.00
95_I 184_S 0.81 0.16 0.00
93_D 70_P 0.81 0.16 0.00
30_A 5_A 0.81 0.16 0.00
2_S 155_L 0.81 0.16 0.00
66_I 157_V 0.81 0.16 0.00
38_A 47_R 0.81 0.16 0.00
64_Q 40_A 0.81 0.16 0.00
61_K 125_L 0.81 0.16 0.00
16_T 117_Q 0.80 0.16 0.00
51_A 19_P 0.80 0.16 0.00
81_T 135_L 0.79 0.15 0.00
95_I 40_A 0.79 0.15 0.00
21_I 26_A 0.79 0.15 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
HHsearch results
2g38BD:ACContact Map
4i0xAKEIGC:BJHDFL:BJHDFLContact Map
3favAC:AC:BDContact Map
ID Seq/Len Name Options I_Prob Status
0177 0.7 2g38 Δgene:(1, 20) A:(1E-10, 4) B:(1E-10, 4) msa: Jackhmmer (2014_03) 0.01 Done
0176 1.02 2g38 Δgene:(0, ∞) A:(1E-10, 4) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.08 Done
0175 0.7 2g38 Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.03 Done
0174 0.7 2g38 Δgene:(1, 20) A:(1E-10, 4) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.06 Done - Shared
0173 0 2g38 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
0172 0.49 2g38 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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